Application of The Method of Elastic Maps In Analysis of Genetic Texts

Abstract - Method of elastic maps ( http://cogprints.ecs.soton.ac.uk/archive/00003088/ and http://cogprints.ecs.soton.ac.uk/archive/00003919/ ) allows us to construct efficiently 1D, 2D and 3D non-linear approximations to the principal manifolds with different topology (piece of plane, sphere, torus etc.) and to project data onto it. We describe the idea of the method and demonstrate its applications in analysis of genetic sequences. The animated 3D-scatters are available on our web-site: http://www.ihes.fr/~zinovyev/7clusters/ We found the universal cluster structure of genetic sequences, and demonstrated the thin structure of these clusters for coding regions. This thin structure is related to different translational efficiency

FuzzyART: An R Package for ART-based Clustering

Adaptive Resonance Theory (ART) was introduced by Steven Grossberg as a theory of human cognitive information processing (Grossberg 1976, 1980). Extending the capabilities of the ART 1 model, which can learn to categorize patterns in binary data, fuzzy ART as described in (Carpenter, Grossberg, and Rosen 1991) has become one of the most commenly used Adaptive Resonance Theory models (Brito da Silva, Elnabarawy, and Wunsch 2019). By incorporating fuzzy set theroy operators, fuzzy ART is capable of learning from binaray and bounded real valued data. Its advantage over other unsupervised learning algorithms lies in the flexibility of the learning rule. If a given input feature does not resemble a known category satisfactorily, as determined by the vigilance test, a new category is initialized. Hence, the total number of categories (or clusters) is not determined a-priori, like k-means, but chosen in accordance with the data and the context of already learnt representations. This vignette explores the use of the fuzzy ART implementation as provided by the FuzzyART R package

Fuzzy Logic in Collective Robotic Search

One important application of mobile robots is searching a geographical region to locate the origin of a specific sensible phenomenon. We first propose a fuzzy logic approach using a decision table. A novel fuzzy rule based was designed. And then a fuzzy search strategy is adopted by utilizing the three tier centers of mass coordination. Experimental results show that fuzzy logic algorithm is an efficient approach for the collective robots to locate the target source. In addition, noise and the position of the target affect the searching result

Engine Data Classification with Simultaneous Recurrent Network using a Hybrid PSO-EA Algorithm

We applied an architecture which automates the design of simultaneous recurrent network (SRN) using a new evolutionary learning algorithm. This new evolutionary learning algorithm is based on a hybrid of particle swarm optimization (PSO) and evolutionary algorithm (EA). By combining the searching abilities of these two global optimization methods, the evolution of individuals is no longer restricted to be in the same generation, and better performed individuals may produce offspring to replace those with poor performance. The novel algorithm is then applied to the simultaneous recurrent network for the engine data classification. The experimental results show that our approach gives solid performance in categorizing the nonlinear car engine data

A Comparison of Dual Heuristic Programming (DHP) and Neural Network Based Stochastic Optimization Approach on Collective Robotic Search Problem

An important application of mobile robots is searching a region to locate the origin of a specific phenomenon. A variety of optimization algorithms can be employed to locate the target source, which has the maximum intensity of the distribution of some detected function. We propose two neural network algorithms: stochastic optimization algorithm and dual heuristic programming (DHP) to solve the collective robotic search problem. Experiments were carried out to investigate the effect of noise and the number of robots on the task performance, as well as the expenses. The experimental results showed that the performance of the dual heuristic programming (DHP) is better than the stochastic optimization method

Speeding Up VLSI Layout Verification Using Fuzzy Attributed Graphs Approach

Technical and economic factors have caused the field of physical design automation to receive increasing attention and commercialization. The steady down-scaling of complementary metal oxide semiconductor (CMOS) device dimensions has been the main stimulus to the growth of microelectronics and computer-aided very large scale integration (VLSI) design. The more an Integrated Circuit (IC) is scaled, the higher its packing density becomes. For example, in 2006 Intel\u27s 65-nm process technology for high performance microprocessor has a reduced gate length of 35 nanometers. In their 70-Mbit SRAM chip, there are up to 0.5 billion transistors in a 110 mm2 chip size with 3.4 GHz clock speed. New technology generations come out every two years and provide an approximate 0.7 times transistor size reduction as predicted by Moore\u27s Law. For the ultimate scaled MOSFET beyond 2015 or so, the transistor gate length is projected to be 10 nm and below. The continually increasing size of chips, measured in either area or number of transistors, and the wasted investment involving fabricating and testing faulty circuits, make layout analysis an important part of physical design automation. Layout-versus-schematic (LVS) is one of three kinds of layout analysis tools. Subcircuit extraction is the key problem to be solved in LVS. In LVS, two factors are important. One is run time, the other is identification correctness. This has created a need for computational intelligence. Fuzzy attributed graph is not only widely used in the fields of image understanding and pattern recognition, it is also useful to the fuzzy graph matching problem. Since the subcircuit extraction problem is a special case of a general-interest problem known as subgraph isomorphism, fuzzy attributed graphs are first effectively applied to the subgraph isomorphism problem. Then we provide an efficient fuzzy attributed graph algorithm based on the solution to subgraph isomorphism for the subcircuit extractio- n problem. Similarity measurement makes a significant contribution to evaluate the equivalence of two circuit graphs. To evaluate its performance, we compare fuzzy attributed graph approach with the commercial software called SubGemini, and two of the fastest approaches called DECIDE and SubHDP. We are able to achieve up to 12 times faster performance than alternatives, without loss of accurac

Outsmart Moore’s Law with Machine Learning

Over the last half century, computing has transformed most aspects of society due to a rapid increase in computation power. With the possible end of Moore’s Law in sight, much of this growth could come to an end. This paper will discuss why machine learning will continue growing even after Moore’s Law, and demonstrate why it is a great time to enter the field

ART/SOFM: A Hybrid Approach to the TSP

We present a new method of solving large scale travelling salesman problem (TSP) instances using a combination of adaptive resonance theory (ART) and self organizing feature maps (SOFM). We divide our algorithm into three phases: phase one uses ART to form clusters of cities; phase two uses a novel modification of the traditional SOFM algorithm to solve a slight variant of the TSP in each cluster of cities; and phase three uses another version of the SOFM to link all the clusters. The experimental results show that our algorithm finds approximate solutions which are about 13% longer than those reported by the chained Lin Kernighan method for problem sizes of 14,000 citie